To recover input tax, a business must normally hold a VAT invoice that shows the particulars in Notice 700, and the supplier's VAT registration number is on that list for a structural reason: only a VAT-registered supplier can charge VAT at all. An amount labelled "VAT" on an invoice from an unregistered trader isn't VAT; there is no input tax to recover, however convincing the paperwork looks.
What happens when the invoice is defective
Where an invoice is missing required particulars, HMRC does have discretion to accept alternative evidence that the supply took place and VAT was due (the discretion sits in regulation 29(2) of the VAT Regulations 1995). But discretion is exactly that: it puts the burden on you, after the fact, usually during an inspection, to reconstruct what a complete invoice would have shown.
The cheaper path is to catch the defect when the invoice arrives: ask the supplier for a corrected document while the transaction is fresh, not four quarters later.
The practical checklist
- Is the supplier's VAT number present on the invoice itself?
- Is it plausibly formatted for the supplier's country?
- Is it actually on the register (HMRC's Check-a-UK-VAT-number service for GB, VIES for EU), and does the registered name match who you think you're paying?
Those three questions are NoticeDesk's Supplier VAT Number, VAT Number (format) and VAT Registration checks. (In NoticeDesk, the register lookup runs against VIES for EU numbers and HMRC's Check-a-UK-VAT-number service for GB; a lookup that can't be completed is recorded as unverified.) The third is also your best early warning against missing-trader fraud in the supply chain.